New Structural Insights into the Genome and Minor Capsid Proteins of BK Polyomavirus using Cryo-Electron Microscopy

Abstract

BK polyomavirus is the causative agent of several diseases in transplant patients and the immunosuppressed. In order to better understand the structure and life cycle of BK, we produced infectious virions and VP1-only virus-like particles in cell culture, and determined their three-dimensional structures using cryo-electron microscopy (EM) and single-particle image processing. The resulting 7.6-Å resolution structure of BK and 9.1-Å resolution of the virus-like particles are the highest-resolution cryo-EM structures of any polyomavirus. These structures confirm that the architecture of the major structural protein components of these human polyomaviruses are similar to previous structures from other hosts, but give new insight into the location and role of the enigmatic minor structural proteins, VP2 and VP3. We also observe two shells of electron density, which we attribute to a structurally ordered part of the viral genome, and discrete contacts between this density and both VP1 and the minor capsid proteins.

Graphical abstract

Figure 1

Purified Virions Are Infectious (A) Vero cell lysate and 30 μl of growth media were analyzed by western blotting to determine the presence of VP1 capsid protein and GAPDH expression. (B) The lysate from RPTE cells infected by gradient purified virions was separated by SDS-PAGE and analyzed by western blotting for the VP1 and VP2/VP3 capsid proteins. (C) RPTE cells were grown on glass coverslips and infected with virions; 3-dpi slides were fixed with 4% paraformaldehyde and stained with antibodies against VP1 (green) and VP2/VP3 (red). The nuclei were visualized with DAPI (blue). Scale bars, 10 μm. (D) Negative-stain electron micrograph of virions present in the Vero cell lysate. (E) Partially purified virions following centrifugation through a cesium chloride gradient. (F) Purified virions following final purification step through a centrifugal concentrator (right). (G) Purified virions suspended in a layer of vitreous ice following cryo-grid preparation. Scale bars, 100 nm.

Figure 2

BK Polyomavirus VLP Production in HEK293TT Cells BK Polyomavirus VLPs produced in HEK293TT cells can package plasmid DNA and can be used as a gene delivery vector. (A) Western blot for VP1 expression in each fraction from the iodixonal gradient. 20 μl of the gradient solution was loaded and VP1 levels were detected using a VP1-specific antibody. (B) Purified VLPs were used to transduce HEK293TT, and the presence of EGFP was analyzed by light microscopy. The image is representative and approximately 65% of the cells were transduced. (C) Negative-stain micrograph of purified VLPs. (D) Cryo-electron micrograph of purified VLPs suspended in vitreous ice. Scale bars, 100 nm.

Figure 3

The Cryo-EM Structures of the BK Virion and VLP (A) An external view of the virion (left) and VLP (right) shown at contour levels of 0.022 and 0.009, respectively. The electron density maps have been sharpened using a negative B factor correction of (B = −456 and −804 Å²), and the density is colored using a radial scheme shown in Ångströms. (B) The architecture of a polyomavirus capsid showing how the T = 7d capsid is built from 72 pentamers of VP1, and an identical VP1 polypeptide sequence is found in six distinct quasi-equivalent conformations in the capsid shell (1, red; 2, yellow; 3, green; 4, cyan; 5, blue; and 6, gray). (C) The cryo-EM structure of the virion (left) and VLP (right) colored according to the scheme in (B), showing the arrangement of different VP1 molecules in three dimensions.

Figure 4

Minor Capsid Proteins and Genome Organization (A) A 40-Å thick slab through the unsharpened/unmasked virion map shown at a contour level of 0.0034. Pyramidal density below each VP1 penton and two shells of electron density adjacent to the inner capsid layer can be seen. The density within 6 Å of the fitted coordinates for SV40 VP1 is colored gray. The remaining density is colored in a radial color scheme. Density for VP2 and VP3 is colored blue→green, and for packaged dsDNA yellow→pink. (B) Enlarged view of the pyramidal density beneath a single VP1 penton of the virion shown at a contour level of 0.0032. Strands of dsDNA wrapped around a human histone octamer (PDB: 1AOI) are shown, indicating that the two shells of density have a comparable spacing. Discrete connective density between the pyramidal density and internal shells is also apparent. Scale bars shown. (C) A 40-Å thick slab through the unsharpened/unmasked VLP map shown at a contour level of 0.0011 which shows that density for the minor capsid proteins and two shells of electron density is absent.

Figure 5

Visualization of Interactions between VP1 N Termini and Encapsidated Genome (A) The location of VP1 N termini binding to the viral genome relative to the minor capsid proteins, viewed down the capsid threefold axis of symmetry (chain color key shown). For visual clarity, density within 6 Å of the fitted coordinates for SV40 VP1 has been removed. A single asymmetric unit from the SV40 atomic model, colored according to the schematic shown in Figure 3B, was fitted as a rigid body into the unsharpened/unmasked virion map. The map was then segmented within 15 Å of the fitted model. (B–G) 20-Å thick slabs of density through the segmented map showing connective bridges of density between the capsid and packaged genome. Each of these is located beneath the N termini of each of the six VP1 quasi-equivalent conformers, which are denoted by asterisks (map contour levels shown).